AP Biology: Evolution Big Idea 1 Investigation 3: Comparing DNA Sequences to Understand Evolutionary Relationships with Blast

Problem: How can bioinformatics be used as a tool to determine evolutionary relationships and to better understand genetic diseases?

Background: (Read the background on the packet and summarize it for your lab notebook)

(Copy the investigations and getting started headings into your lab notebooks) The Investigations:

Getting Started: (Answer the getting started questions #1-2 (a & b) into your lab notebooks)

Procedure: (Write the procedure heading and tape in the fossil picture, do as the procedure indicates and then write a summary of the activity)

Step 1: (Tape in the fossil cladogram and follow the instructions)

Step 2: Download files. Locate and download gene files. Step 3: Upload the gene sequences into BLAST. (Record what BLAST stands for in your lab notebook) http://blast.ncbi.nlm.nih.gov/Blast.cgi

Procedure for Step 2 and 3: Below are the gene files to use for Investigative Lab 3. Note that the files do not open on your computer. You must click on the files, and download them by clicking, 'Download' and then save. Once the zip file is saved, you should then unpack it by saving the individual file. Then you must go to the BLAST site and 1. Click on the 'Saved Strategies' from the menu at the top of the page 2. Under "Upload Search Strategy", click on "Browse" and locate one of the gene files you saved onto your computer 3. Click "View" A screen will appear with the parameters for your query already configured. NOTE: Do not alter any of the parameters. Scroll down the page and click on the "BLAST" button at the bottom. After collecting and analyzing all of the data for that particular gene, repeat this procedure for the other two gene sequences. ● Gene 1

● Gene 2

● Gene 3

● Gene 4 Step 4: Results (Collect information from BLAST for each of the gene files, you should be thinking about your original hypothesis and whether the data support or cause you to reject your original placement of the fossil species on the cladogram.) ● The higher the score, the closer the alignment. ● The lower the e value, the closer the alignment. ● Sequences with e values less than 1e-04 (1x10-4) can be considered related with an error rate of less than 0.01%. Case File 1: Case File 2: Case File 3: Case File 4:

Analyzing Results (Answer questions 1-4 in your lab notebooks and follow the instructions after question 4.)

Evaluating Results (Do all that is listed)

Designing and Conducting Your Investigation (Document the following in your lab notebook.)

Select a gene of interest from the suggestions on the lab or find one on your own using the Entrez Gene website: http://www.ncbi.nlm.nih.gov/gene to conduct your own investigation.

Develop a starting question based on your gene then follow the example procedures in the AP packet to investigate it. Document your work/findings in your lab notebook as you work through your investigation. Prepare a simple presentation to share with the class about your gene.

Answer the bulleted analysis and conclusion questions in full sentences in your lab notebook.